[spctools-discuss] Re: Unresolved issue: TPP GUI error message: sh: tpp_hostname: command not found
OK yeah fixing the document root was all that I needed. I was wondering why I had it set to that but I think it was some configuration settings someone suggested to me when I was having some other probs but all seems fine now. Thanks! On Jun 15, 7:31 pm, Natalie Tasman natalie.tas...@insilicos.com wrote: Hi Eliza, The file being referenced is supposed to be /usr/local/tpp/data (according to the full filename passed to the pepXML viewer CGI). But according to your previously-posted check_env results, your webserver's document root is /usr/local/tpp/html/. That typically means that anything your webserver can display must be under /usr/local/tpp/html/. That's possibly why the error message says can't find /usr/local/tpp/^^^html^^^/data when the file to display was under /usr/local/tpp/data. [And echoing Brian and other's comments about making sure the user which Apache is running as has full read and write access down through all of your data directories.] Hope this helps, Natalie On 6/15/10 6:22 AM, Eliza wrote: Well there does so happen to be an error in the Apache log file... [Thu Jun 03 11:10:25 2010] [error] [client xxx.xxx.xx.xx] File does not exist: /usr/local/tpp/html/data, referer: http://localhost/tpp/cgi-bin/PepXMLViewer.cgi?xmlFileName=/usr/local/... but would this be coming from the PepXMLViewer.cgi file which is a bit difficult to read as it is binary? On Jun 1, 11:34 pm, Joe Slagel jsla...@systemsbiology.org wrote: Eliza, There is a javascript check in the viewer the periodically checks to see if the file on the server has changed relative to what is being displayed. What the message indicates is that it was unable to retrieve the timestamp for the file. This shouldn't be too significant of a problem as you still should be able to view the file. There can be a number of different reasons for the file check to fail. Probably the first place to look at is the apache log files -- your server may be blocking HEAD requests, or the URL to the file may be incorrect. -Joe On Mon, May 31, 2010 at 4:35 AM, Eliza blond...@googlemail.com wrote: OK so I was able to figure out how how to set the PATH for the webserver user and eradicated that error. That still leaves me with the following error in the browser: Unable to access xml file via webserver, so cannot check xml file for changes () Check webserver configuration if desired. (URL: undefined) Suggestions on what I need to look at to fix this? On May 24, 7:39 pm, Brian Pratt brian.pr...@insilicos.com wrote: PATH = /usr/local/bin:/usr/bin:/bin Doesn't seem to include your TPP executables. You'll need to figure out how to update that for the Apache process user. On Mon, May 24, 2010 at 12:39 AM, Eliza blond...@googlemail.com wrote: Here is the output (with some details removed) SCRIPT_NAME = /tpp/cgi-bin/check_env.pl SERVER_NAME = servername SERVER_ADMIN = webmas...@localhost HTTP_ACCEPT_ENCODING = gzip,deflate HTTP_CONNECTION = keep-alive REQUEST_METHOD = GET HTTP_ACCEPT = text/html,application/xhtml+xml,application/xml;q=0.9,*/ *;q=0.8 SCRIPT_FILENAME = /usr/local/tpp/cgi-bin/check_env.pl SERVER_SOFTWARE = Apache/2.2.3 (Debian) PHP/5.2.0-8+etch16 HTTP_ACCEPT_CHARSET = ISO-8859-1,utf-8;q=0.7,*;q=0.7 QUERY_STRING = REMOTE_PORT = 3975 HTTP_USER_AGENT = Mozilla/5.0 (Windows; U; Windows NT 5.1; en-US; rv: 1.9.1.9) Gecko/20100315 Firefox/3.5.9 ( .NET CLR 3.5.30729) SERVER_PORT = 80 SERVER_SIGNATURE = Apache/2.2.3 (Debian) PHP/5.2.0-8+etch16 Server at server Port 80 HTTP_ACCEPT_LANGUAGE = en-us,en;q=0.5 REMOTE_ADDR = xx.xx.xx.xx WEBSERVER_ROOT = /usr/local/tpp HTTP_KEEP_ALIVE = 300 SERVER_PROTOCOL = HTTP/1.1 PATH = /usr/local/bin:/usr/bin:/bin REQUEST_URI = /tpp/cgi-bin/check_env.pl GATEWAY_INTERFACE = CGI/1.1 SERVER_ADDR = 130.232.69.141 DOCUMENT_ROOT = /usr/local/tpp/html/ WEBSERVER_TMP = /usr/local/tpp/html/tmp HTTP_HOST = host On May 21, 3:15 am, Brian Pratt brian.pr...@insilicos.com wrote: PATH is of interest as well. Or you could just paste all the results into a message to this list. On Thu, May 20, 2010 at 7:38 AM, Vishal Swaroop vishal@gmail.com wrote: As I have not configured TPP on linux so I am not sure if I will be of help but check WEBSERVER_ROOT and SCRIPT_FILENAME = path to tppbin/check_env.pl See, if path to tppbin in SCRIPT_FILENAME is set in apache configuration file httpd.conf. As per your post description, does it mean that you are able to login and run some of the process from gui, on what event/ click you get this error, which browser you are using ? Thanks On Thu, May 20, 2010 at 4:42 AM, Eliza blond...@googlemail.com wrote: The webserver is working fine, it is used to host a couple other sites and they aren't experiencing any issues :-) I ran check_env.pl but I am not sure what I should which values I
Re: [spctools-discuss] installing some programs in standalone
Sure, that's not unusual. Have a look at the makefile to see the individual targets. Building on Solaris 10 *is* a bit unusual, though, you may hit some bumps. On Thu, Jun 17, 2010 at 4:17 AM, sasircm duha...@ircm.qc.ca wrote: Hello I would like to intergrate some of TPP programs in a in house pipeline. Is it possible to compile only the required programs, or do I have to install the whole package? If possible, how should I proceed? I am on Solaris 10 Thank you -- You received this message because you are subscribed to the Google Groups spctools-discuss group. To post to this group, send email to spctools-disc...@googlegroups.com. To unsubscribe from this group, send email to spctools-discuss+unsubscr...@googlegroups.comspctools-discuss%2bunsubscr...@googlegroups.com . For more options, visit this group at http://groups.google.com/group/spctools-discuss?hl=en. -- You received this message because you are subscribed to the Google Groups spctools-discuss group. To post to this group, send email to spctools-disc...@googlegroups.com. To unsubscribe from this group, send email to spctools-discuss+unsubscr...@googlegroups.com. For more options, visit this group at http://groups.google.com/group/spctools-discuss?hl=en.
[spctools-discuss] About Database in Mascot search in TPP (attachment)
Hi, I can't make attachment with my last email, so I send one more about my error messages. 1. The data folder only contain one mzXML file and its mascot.dat file (searched again used current SwissProt 57.12 database in our in-house Mascot server) got: c:/Inetpub/wwwroot/ISB/data/SSM4-1/F030337.pep.xml [ Unreadable! ] run_in c:/Inetpub/wwwroot/ISB/data/SSM4-1; c:\Inetpub\tpp-bin \Mascot2XML c:/Inetpub/wwwroot/ISB/data/SSM4-1/F030337.dat -Dc:/ Inetpub/wwwroot/ISB/data/SwissProt_57.12.fasta -Etrypsin filepath: c:/Inetpub/wwwroot/ISB/data/SSM4-1/, extn: F030337 A stored as 71.0371 B stored as 114.535 C stored as 103.009 D stored as 115.027 E stored as 129.043 F stored as 147.068 G stored as 57.0215 H stored as 137.059 I stored as 113.084 J stored as 0 K stored as 128.095 L stored as 113.084 M stored as 131.04 N stored as 114.043 O stored as 0 P stored as 97.0528 Q stored as 128.059 R stored as 156.101 S stored as 87.032 T stored as 101.048 U stored as 150.954 V stored as 99.0684 W stored as 186.079 X stored as 111 Y stored as 163.063 Z stored as 128.551 c stored as 17.0027 n stored as 1.00782 variable modification 1, delta mass 227.127 for ICAT-C (C): residues: C nterm: 0 cterm: 0 protterm: 0 variable modification 2, delta mass 236.157 for ICAT-C:13C(9) (C): residues: C nterm: 0 cterm: 0 protterm: 0 variable modification 3, delta mass 15.9949 for Oxidation (M): residues: M nterm: 0 cterm: 0 protterm: 0 trypsin : cut(KR) nocuts(P) sense(C) command c:\Inetpub\tpp-bin\Mascot2XML c:/Inetpub/wwwroot/ISB/data/ SSM4-1/F030337.dat -Dc:/Inetpub/wwwroot/ISB/data/SwissProt_57.12.fasta -Etrypsin failed: Operation not permitted Command FAILED 2. The data fold contain one mzXML file and its Mascot.pepxml file. I directly used “Analysis Pipeline (Mascot) / Analyze Peptides” got c:/Inetpub/wwwroot/ISB/data/SSM_4_1/SSM4-1.pep.shtml [ View ] run_in c:/Inetpub/wwwroot/ISB/data/SSM_4_1; c:\Inetpub\tpp-bin \xinteract -NSSM4-1.pep.xml -p0.05 -l7 -Oi -X-m1.0-nC,9.0 -A-lC-r0.5 c:/Inetpub/wwwroot/ISB/data/SSM_4_1/F028529-2.xml c:\Inetpub\tpp-bin\xinteract (TPP v4.3 JETSTREAM rev 1, Build 200909091257 (MinGW)) running: C:/Inetpub/tpp-bin/InteractParser SSM4-1.pep.xml c:/ Inetpub/wwwroot/ISB/data/SSM_4_1/F028529-2.xml -L7 file 1: c:/Inetpub/wwwroot/ISB/data/SSM_4_1/F028529-2.xml processed altogether 337 results results written to file c:/Inetpub/wwwroot/ISB/data/SSM_4_1/ SSM4-1.pep.xml direct your browser to http://localhost/ISB/data/SSM_4_1/SSM4-1.pep.shtml command completed in 1 sec running: C:/Inetpub/tpp-bin/PeptideProphetParser SSM4-1.pep.xml MINPROB=0.05 ICAT (MASCOT) (icat) error: -1.0 ion score command C:/Inetpub/tpp-bin/PeptideProphetParser SSM4-1.pep.xml MINPROB=0.05 ICAT failed: Operation not permitted command C:/Inetpub/tpp-bin/PeptideProphetParser SSM4-1.pep.xml MINPROB=0.05 ICAT exited with non-zero exit code: 1 QUIT - the job is incomplete command c:\Inetpub\tpp-bin\xinteract -NSSM4-1.pep.xml -p0.05 -l7 -Oi - X-m1.0-nC,9.0 -A-lC-r0.5 c:/Inetpub/wwwroot/ISB/data/SSM_4_1/ F028529-2.xml failed: Operation not permitted Command FAILED 3. The data fold contain one mzXML file and its Mascot.xml file. I directly used “Analysis Pipeline (Mascot) / Analyze Peptides” got c:/Inetpub/wwwroot/ISB/data/SSM_4_1/SSM4-1.pep.shtml [ View ] CAN NOT open the pepxml viewer in TPP run_in c:/Inetpub/wwwroot/ISB/data/SSM_4_1; c:\Inetpub\tpp-bin \xinteract -NSSM4-1.pep.xml -p0.05 -l7 -Oi -X-m1.0-nC,9.0 -A-lC-r0.5 c:/Inetpub/wwwroot/ISB/data/SSM_4_1/F028529.xml c:\Inetpub\tpp-bin\xinteract (TPP v4.3 JETSTREAM rev 1, Build 200909091257 (MinGW)) running: C:/Inetpub/tpp-bin/InteractParser SSM4-1.pep.xml c:/ Inetpub/wwwroot/ISB/data/SSM_4_1/F028529.xml -L7 file 1: c:/Inetpub/wwwroot/ISB/data/SSM_4_1/F028529.xml processed altogether 0 results ERROR: output file created, c:/Inetpub/wwwroot/ISB/data/SSM_4_1/ SSM4-1.pep.xml, appears incomplete. Please check the input files for completeness. results written to file c:/Inetpub/wwwroot/ISB/data/SSM_4_1/ SSM4-1.pep.xml direct your browser to http://localhost/ISB/data/SSM_4_1/SSM4-1.pep.shtml command completed in 0 sec running: C:/Inetpub/tpp-bin/PeptideProphetParser SSM4-1.pep.xml MINPROB=0.05 ICAT MS Instrument info: Manufacturer: UNKNOWN, Model: UNKNOWN, Ionization: UNKNOWN, Analyzer: UNKNOWN, Detector: UNKNOWN error: no peptideprophet data written to file SSM4-1.pep.xml Error: file update failed, check file SSM4-1.pep.xml.tmp.a02524 for completeness command C:/Inetpub/tpp-bin/PeptideProphetParser SSM4-1.pep.xml MINPROB=0.05 ICAT failed: Operation not permitted command C:/Inetpub/tpp-bin/PeptideProphetParser SSM4-1.pep.xml MINPROB=0.05 ICAT exited with non-zero exit code: 1 QUIT - the job is incomplete command c:\Inetpub\tpp-bin\xinteract -NSSM4-1.pep.xml -p0.05 -l7 -Oi - X-m1.0-nC,9.0 -A-lC-r0.5
